Identification of biomolecules is routine in biopharmaceutical and proteomics research. Current commercial mass spectrometers can be equipped with collision cells that employ quadrupoles or multipoles in which ion fragmentation occurs by a process known as collision-induced dissociation (CID). Conventional CID is a process in which ions are accelerated by an electric field to increase the ion kinetic energy. Upon collision with a buffer gas, the ions fragment. In these conventional devices, CID occurs at the entrance of the quadrupole, where ion scattering at the ends of the quadrupole rods and strength of the DC field gradient are the greatest. Fragmentation can also take place inside the quadrupole, but fragmentation efficiency strongly depends on the quadrupole pressure, as kinetic energy dampening due to collisions is significant while the electric field inside the quadrupole is zero. CID in conventional quadrupoles often suffers from poor fragmentation and poor collection efficiencies because of: 1) a relatively low operation pressure (typical pressures are 1-5 mTorr), 2) few collisions per unit length, 3) a low collision energy in the center-of-mass frame that limits activation of larger molecules, and 4) because fragment ions produced in RF-fringing fields at the quadrupole entrance can be easily lost due to scattering. For example, collection efficiencies for multiple-charged species in triple-quadrupole instruments have typical best values between 10% and 17%.
The primary purpose of RF fields in conventional devices is to radially confine ions. In some applications, RF fields can be used to cause ion instability that result in increased radial oscillations of precursor ions. In this case, all ions with an m/z below that of the precursor become unstable, meaning one can only detect fragments with an m/z above that of the precursor. For multiply-charged ions, this means that up to a full half of useful structural information can be lost in a mass spectrum. As a result, poor fragmentation patterns occur, and insufficient structural information is obtained to ascertain required sequencing information by which to unambiguously identify molecules of interest. If the internal energy content of the parent (primary precursor) ions is high, some fraction of the parent ions will gain sufficient energy to fragment further, producing secondary fragments from the primary fragments, which proves to be of little value for structural determination of complex ions. For example, in conventional devices, precursor ions typically dissociate in close proximity to the quadrupole entrance, resulting in fragment ions that impart additional activation energy further downstream in the quadrupole, which results in secondary fragments that provide little structural information or that gives rise to uninformative spectra. In addition, in conventional MS/MS, activation of singly-charged precursor ions requires higher electric, fields, which also results in secondary fragmentation of fragments produced by multiply-charged ions of the same species, which again provides little useful information for structural determination of ions. While conventional activation methodologies and devices provide some fragmentation data, ultimately, in excess of 25% of large bio-molecules including, e.g., proteins and peptides, are estimated to remain unidentified in conventional tandem MS/MS experiments using, e.g., conventional triple-quadrupole instruments. Triple-quadrupole instruments can fail to characterize and identify complex molecules due to an inability to provide sufficient structure-specific fragments for the molecules of interest. Accordingly, new systems and methods are needed that increase the fragmentation efficiencies necessary to producing an abundance of structurally-rich fragment ions by which to identify complex molecules.